Averaging Mass Spectra - Revision history

Laschp: /* Producing average spectra */

2025-03-27T14:20:06Z

Producing average spectra

← Older revision		Revision as of 16:20, 27 March 2025
Line 4:		Line 4:

	== Producing average spectra ==		== Producing average spectra ==
	~~<br>~~

	: 1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.		1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.

	: 2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.		2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.

	: 3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' --> ''class X'' from the ''Edit'' pull down menu.		3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' --> ''class X'' from the ''Edit'' pull down menu.

	: 4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.		4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.

Laschp at 14:18, 27 March 2025

2025-03-27T14:18:38Z

← Older revision		Revision as of 16:18, 27 March 2025
Line 1:		Line 1:
	~~Various~~ reasons ~~exist to create average, or mean spectra, from~~ individual mass spectra. First and foremost, averaging allows ~~to improve~~ the spectral signal-to-noise ratio (SNR). A second ~~goal~~ of spectra ~~averaging~~ is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, ~~spectra~~ averaging ~~may~~ be useful when ~~prepraring~~ illustrations for presentations or scientific publications.		There are several reasons for averaging individual mass spectra. First and foremost, averaging allows the spectral signal-to-noise ratio (SNR) to be improved. A second purpose of averaging spectra is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectral averaging can be useful when preparing illustrations for presentations or scientific publications.

	'''IMPORTANT''': Average spectra should not be used as inputs for identification algorithms. For this purpose please use the function [[Create database spectra\|create database spectra from individual microbial mass spectra]].		'''IMPORTANT''': Average spectra should not be used as inputs for identification algorithms. For this purpose please use the function [[Create database spectra\|create database spectra from individual microbial mass spectra]].

	== Producing average spectra ==		== Producing average spectra ==
			<br>

	: 1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.		: 1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.

Laschp: /* Producing average spectra */

2025-03-27T14:17:15Z

Producing average spectra

← Older revision		Revision as of 16:17, 27 March 2025
Line 6:		Line 6:


	::1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.		: 1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.

	:2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.		: 2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.

	:3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' --> ''class X'' from the ''Edit'' pull down menu.		: 3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' --> ''class X'' from the ''Edit'' pull down menu.

	:4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.		: 4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.

Laschp: /* Producing average spectra */

2025-03-27T14:16:57Z

Producing average spectra

← Older revision		Revision as of 16:16, 27 March 2025
Line 6:		Line 6:


	:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.		::1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.

	:2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.		:2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.

Laschp: /* Producing average spectra */

2025-03-27T14:16:47Z

Producing average spectra

← Older revision		Revision as of 16:16, 27 March 2025
Line 6:		Line 6:


	:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' ~~pulldown~~ menu.		:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pull down menu.

	:2. To produce an average spectrum select the respective mass spectra in the ~~listbox~~ at the top left corner (the ~~listbox~~ is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.		:2. To produce an average spectrum select the respective mass spectra in the list box at the top left corner (the list box is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.

	:3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. ~~Labelling~~, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class ~~assignements~~'' --> ''class X'' from the ''Edit'' ~~pulldown~~ menu.		:3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labeling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignments'' --> ''class X'' from the ''Edit'' pull down menu.

	:4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.		:4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.

Laschp: /* Producing average spectra */

2025-03-27T14:16:03Z

Producing average spectra

← Older revision		Revision as of 16:16, 27 March 2025
Line 4:		Line 4:

	== Producing average spectra ==		== Producing average spectra ==


	:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.		:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

Laschp: /* Producing average spectra */

2025-03-27T14:15:47Z

Producing average spectra

← Older revision		Revision as of 16:15, 27 March 2025
Line 5:		Line 5:
	== Producing average spectra ==		== Producing average spectra ==

	1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format),		:1. Load the mass spectral data files via the [[Load spectra (Bruker format)\|load spectra]] (Bruker data file format), [[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.
	[[Import Mass Spectra in a mzXML Data Format\|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

	2. To produce an average spectrum select the respective mass spectra in the listbox at the		:2. To produce an average spectrum select the respective mass spectra in the listbox at the top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra hold the <shift> key while selecting.
	top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra
	hold the <shift> key while selecting.

	3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from		:3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra, i.e. from spectra with a [[Class Assignment\|class assignment]]. Labelling, or class assignment, can be carried out by selecting the appropriate spectra and choosing ''class assignements'' --> ''class X'' from the ''Edit'' pulldown menu.
	the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra,
	i.e. from spectra with a [[Class Assignment\|class assignment]]. Labelling, or class assignment, can be carried out
	by selecting the appropriate spectra and choosing ''class assignements'' --> ''class X'' from
	the ''Edit'' pulldown menu.

	4. Average spectra are created by a simple averaging procedure, either from original, or from		:4. Average spectra are created by a simple averaging procedure, either from original, or from pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the ''VIEW'' tab). When averaging is finished a new file id in the format avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum are automatically adopted as the metadata of the average spectrum.
	pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the
	''VIEW'' tab). When averaging is finished a new file id in the format
	avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum
	are automatically adopted as the metadata of the average spectrum.

Laschp: Created page with "Various reasons exist to create average, or mean spectra, from individual mass spectra. First and foremost, averaging allows to improve the spectral signal-to-noise ratio (SNR). A second goal of spectra averaging is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectra averaging may be useful when prepraring illustrations for presentations or scientific publications. '''IMPORTANT''':..."

2023-03-18T09:27:12Z

Created page with "Various reasons exist to create average, or mean spectra, from individual mass spectra. First and foremost, averaging allows to improve the spectral signal-to-noise ratio (SNR). A second goal of spectra averaging is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectra averaging may be useful when prepraring illustrations for presentations or scientific publications. '''IMPORTANT''':..."

New page

Various reasons exist to create average, or mean spectra, from individual mass spectra. First and foremost, averaging allows to improve the spectral signal-to-noise ratio (SNR). A second goal of spectra averaging is to eliminate the degree of spectral variability when measuring spatially inhomogeneous samples from different sample spots. Finally, spectra averaging may be useful when prepraring illustrations for presentations or scientific publications.

'''IMPORTANT''': Average spectra should not be used as inputs for identification algorithms. For this purpose please use the function [[Create database spectra|create database spectra from individual microbial mass spectra]].

== Producing average spectra ==

1. Load the mass spectral data files via the [[Load spectra (Bruker format)|load spectra]] (Bruker data file format),
[[Import Mass Spectra in a mzXML Data Format|import spectra from mzXML data]], or the ''load MS multifile'' options of the ''File'' pulldown menu.

2. To produce an average spectrum select the respective mass spectra in the listbox at the
top left corner (the listbox is labeled by ''MicrobeMS spectra ID`s''). To select multiple spectra
hold the <shift> key while selecting.

3. Start the procedure by selecting ''average spectra'' --> ''from selection'' from
the ''Analysis'' pull down menu. Average spectra can be also created from labeled spectra,
i.e. from spectra with a [[Class Assignment|class assignment]]. Labelling, or class assignment, can be carried out
by selecting the appropriate spectra and choosing ''class assignements'' --> ''class X'' from
the ''Edit'' pulldown menu.

4. Average spectra are created by a simple averaging procedure, either from original, or from
pre-processed mass spectra (depending on the status of the checkbox ''org.spectra'' in the
''VIEW'' tab). When averaging is finished a new file id in the format
avrgspec-DD-MON-YEAR-HR-MI-SE.XXX is created. Note that the metadata from the first spectrum
are automatically adopted as the metadata of the average spectrum.